Spatial transcriptomics and imaging-based omics technologies reveal not just what genes are expressed, but where they are expressed within tissues. The openpipeline_spatial package provides standardized workflows to process data from multiple spatial platforms including 10x Xenium, NanoString CosMx, and 10x Visium.
Convert proprietary formats into standardized H5MU files, perform quality control, and prepare your spatial data for downstream analysis with confidence.
The package currently supports major spatial omics platforms:
The spatial_process_samples workflow handles batch processing of multiple spatial samples with consistent preprocessing steps.
Each spatial platform generates data in different formats with varying metadata structures. By converting to H5MU format, you can: